1rgf
From Proteopedia
(New page: 200px<br /><applet load="1rgf" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rgf, resolution 1.20Å" /> '''HYDROLASE, GUANYLORI...) |
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| - | [[Image:1rgf.gif|left|200px]]<br /><applet load="1rgf" size=" | + | [[Image:1rgf.gif|left|200px]]<br /><applet load="1rgf" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1rgf, resolution 1.20Å" /> | caption="1rgf, resolution 1.20Å" /> | ||
'''HYDROLASE, GUANYLORIBONUCLEASE'''<br /> | '''HYDROLASE, GUANYLORIBONUCLEASE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Crystals of ribonuclease from Streptomyces aureofaciens diffract to atomic | + | Crystals of ribonuclease from Streptomyces aureofaciens diffract to atomic resolution at room temperature. Using synchrotron radiation and an imaging-plate scanner, X-ray data have been recorded to 1.20 A resolution from a crystal of native enzyme and to 1.15 A from a crystal of a complex with guanosine-2'-monophosphate. Refinement with anisotropic atomic temperature factors resulted in increased accuracy of the structure. The R factors for the two structures are 10.6 and 10.9%. The estimated r.m.s. error in the coordinates is 0.05 A, less than half that obtained in the previous analysis at 1.7 A resolution. For the well ordered part of the main chain the error falls to below 0.02 A as estimated from inversion of the least-squares matrix. The two independent molecules in the asymmetric unit allowed detailed analysis of peptide planarity and some torsion angles. The high accuracy of the analysis revealed density for a partially occupied anion in the nucleotide binding site of molecule A in the native structure which was not seen at lower resolution. The anisotropic model allowed correction of the identity of the residue at position 72 from cysteine to threonine. Cys72 SG had been modelled in previous analyses with two conformations. The solvent structure was modelled by means of an automated procedure employing a set of objective criteria. The solvent structure for models refined using different programs with isotropic and anisotropic description of thermal motion is compared. |
==About this Structure== | ==About this Structure== | ||
| - | 1RGF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_aureofaciens Streptomyces aureofaciens] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] Full crystallographic information is available from [http:// | + | 1RGF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_aureofaciens Streptomyces aureofaciens] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RGF OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Streptomyces aureofaciens]] | [[Category: Streptomyces aureofaciens]] | ||
[[Category: Dauter, Z.]] | [[Category: Dauter, Z.]] | ||
| - | [[Category: Lamzin, V | + | [[Category: Lamzin, V S.]] |
[[Category: Sevcik, J.]] | [[Category: Sevcik, J.]] | ||
| - | [[Category: Wilson, K | + | [[Category: Wilson, K S.]] |
[[Category: SO4]] | [[Category: SO4]] | ||
[[Category: hydrolase (guanyloribonuclease)]] | [[Category: hydrolase (guanyloribonuclease)]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:50:36 2008'' |
Revision as of 12:50, 21 February 2008
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HYDROLASE, GUANYLORIBONUCLEASE
Overview
Crystals of ribonuclease from Streptomyces aureofaciens diffract to atomic resolution at room temperature. Using synchrotron radiation and an imaging-plate scanner, X-ray data have been recorded to 1.20 A resolution from a crystal of native enzyme and to 1.15 A from a crystal of a complex with guanosine-2'-monophosphate. Refinement with anisotropic atomic temperature factors resulted in increased accuracy of the structure. The R factors for the two structures are 10.6 and 10.9%. The estimated r.m.s. error in the coordinates is 0.05 A, less than half that obtained in the previous analysis at 1.7 A resolution. For the well ordered part of the main chain the error falls to below 0.02 A as estimated from inversion of the least-squares matrix. The two independent molecules in the asymmetric unit allowed detailed analysis of peptide planarity and some torsion angles. The high accuracy of the analysis revealed density for a partially occupied anion in the nucleotide binding site of molecule A in the native structure which was not seen at lower resolution. The anisotropic model allowed correction of the identity of the residue at position 72 from cysteine to threonine. Cys72 SG had been modelled in previous analyses with two conformations. The solvent structure was modelled by means of an automated procedure employing a set of objective criteria. The solvent structure for models refined using different programs with isotropic and anisotropic description of thermal motion is compared.
About this Structure
1RGF is a Single protein structure of sequence from Streptomyces aureofaciens with as ligand. Active as Ribonuclease T(1), with EC number 3.1.27.3 Full crystallographic information is available from OCA.
Reference
Ribonuclease from Streptomyces aureofaciens at atomic resolution., Sevcik J, Dauter Z, Lamzin VS, Wilson KS, Acta Crystallogr D Biol Crystallogr. 1996 Mar 1;52(Pt 2):327-44. PMID:15299705
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